EHV-1 TSS dynamics
Balázs Kakuk
## Error in library(future.apply) :
## there is no package called 'future.apply'Project info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Normalization: NO (raw read counts)
TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.8)... Done.## Bootstrap (r = 0.9)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Cut the tree at an optimal number of clusters
Clustering statistics: Cluster number: 5
## [1] "CTO" "ORF8" "ORF49" "ORF42" "ORF40" "ORF36" "ORF46"
## [8] "ORF24" "ORF44" "ORF56" "NOIR_2" "ORF23" "ORF43" "ORF58"
## [15] "ORF22" "ORF51" "ORF1" "ORF68" "ORF28" "ORF59" "ORF74"
## [22] "ORF70" "ORF39" "NOIR_1" "ORF75" "ORF9" "ORF55" "ORF38"
## [29] "ORF20" "ORF67_1" "ORF66_1" "ORF18" "ORF4" "ORF31" "ORF61"
## [36] "ORF50" "ORF32" "ORF64_1" "ORF7" "ORF76" "ORF21" "ORF19"
## [43] "ORF3" "ORF37" "ORF26" "ORF29" "ORF34" "ORF17" "ORF2"
## [50] "ORF65_1" "ORF14" "ORF69" "ORF11" "ORF5" "ORF73" "ORF12"
## [57] "ORF13" "ORF16" "ORF71" "ORF52" "ORF72" "ORF54" "ORF6"
## [64] "ORF57" "ORF41" "ORF35" "ORF60" "ORF10" "ORF15" "ORF62"
## [71] "ORF27" "ORF48" "ORF35.5" "ORF25" "ORF33" "ORF30" "ORF63"
## [78] "ORF53" "ORF45"## [1] 79Clustering statistics: Cluster number: 6
## [1] "ORF42" "ORF49" "ORF36" "ORF40" "ORF8" "ORF56" "ORF44"
## [8] "CTO" "ORF24" "ORF23" "ORF46" "ORF43" "ORF68" "ORF22"
## [15] "ORF74" "ORF70" "ORF39" "ORF1" "ORF28" "ORF58" "NOIR_2"
## [22] "ORF9" "ORF75" "ORF55" "ORF20" "ORF38" "ORF4" "ORF67_1"
## [29] "ORF66_1" "ORF18" "ORF31" "ORF61" "ORF32" "ORF64_1" "ORF50"
## [36] "ORF76" "ORF7" "ORF37" "ORF19" "ORF3" "ORF21" "ORF26"
## [43] "ORF34" "ORF29" "ORF17" "ORF65_1" "ORF2" "ORF69" "ORF14"
## [50] "ORF5" "ORF11" "ORF73" "ORF16" "ORF13" "ORF71" "ORF12"
## [57] "ORF72" "ORF6" "ORF41" "ORF60" "ORF54" "ORF52" "ORF57"
## [64] "ORF35" "ORF10" "ORF15" "ORF27" "ORF62" "ORF48" "ORF35.5"
## [71] "ORF25" "ORF33" "ORF30" "ORF63" "ORF53" "ORF45" "ORF59"
## [78] "ORF51" "NOIR_1"## [1] 79Clustering statistics: Cluster number: 7
## [1] "CTO" "ORF24" "ORF8" "ORF42" "ORF49" "ORF23" "ORF46"
## [8] "ORF43" "ORF44" "ORF40" "ORF36" "ORF56" "ORF22" "ORF58"
## [15] "ORF28" "ORF68" "ORF1" "ORF74" "ORF39" "ORF70" "NOIR_2"
## [22] "ORF18" "ORF38" "ORF50" "ORF20" "ORF61" "ORF21" "ORF3"
## [29] "ORF26" "ORF67_1" "ORF31" "ORF7" "ORF19" "ORF29" "ORF76"
## [36] "ORF34" "ORF2" "ORF32" "ORF66_1" "ORF17" "ORF14" "ORF64_1"
## [43] "ORF11" "ORF73" "ORF65_1" "ORF4" "ORF69" "ORF55" "ORF5"
## [50] "ORF9" "ORF37" "ORF75" "ORF16" "ORF13" "ORF71" "ORF12"
## [57] "ORF72" "ORF6" "ORF41" "ORF60" "ORF54" "ORF52" "ORF57"
## [64] "ORF35" "ORF10" "ORF15" "ORF27" "ORF62" "ORF48" "ORF35.5"
## [71] "ORF25" "ORF33" "ORF30" "ORF63" "ORF53" "ORF45" "ORF59"
## [78] "ORF51" "NOIR_1"## [1] 79Selected number of clusters: 7
## [1] "CTO" "ORF24" "ORF8" "ORF42" "ORF49" "ORF23" "ORF46"
## [8] "ORF43" "ORF44" "ORF40" "ORF36" "ORF56" "ORF22" "ORF58"
## [15] "ORF28" "ORF68" "ORF1" "ORF74" "ORF39" "ORF70" "NOIR_2"
## [22] "ORF18" "ORF38" "ORF50" "ORF20" "ORF61" "ORF21" "ORF3"
## [29] "ORF26" "ORF67_1" "ORF31" "ORF7" "ORF19" "ORF29" "ORF76"
## [36] "ORF34" "ORF2" "ORF32" "ORF66_1" "ORF17" "ORF14" "ORF64_1"
## [43] "ORF11" "ORF73" "ORF65_1" "ORF4" "ORF69" "ORF55" "ORF5"
## [50] "ORF9" "ORF37" "ORF75" "ORF16" "ORF13" "ORF71" "ORF12"
## [57] "ORF72" "ORF6" "ORF41" "ORF60" "ORF54" "ORF52" "ORF57"
## [64] "ORF35" "ORF10" "ORF15" "ORF27" "ORF62" "ORF48" "ORF35.5"
## [71] "ORF25" "ORF33" "ORF30" "ORF63" "ORF53" "ORF45" "ORF59"
## [78] "ORF51" "NOIR_1"## [1] 79Remove genes from clusters ?
## The following genes were removed from their corresponding clusters
## as their silhouette widths were lower than 0.1 and their distance from the group centroid was higher than 0.5:
## CTO
## ORF24
## ORF8
## ORF42
## ORF49
## ORF23
## ORF46
## ORF43
## ORF44
## ORF40
## ORF36
## ORF56
## ORF22
## ORF58
## ORF28
## ORF68
## ORF1
## ORF74
## ORF39
## ORF70
## NOIR_2
## ORF18
## ORF38
## ORF50
## ORF20
## ORF61
## ORF21
## ORF3
## ORF26
## ORF67_1
## ORF31
## ORF7
## ORF19
## ORF29
## ORF76
## ORF34
## ORF2
## ORF32
## ORF66_1
## ORF17
## ORF14
## ORF64_1
## ORF11
## ORF73
## ORF65_1
## ORF4
## ORF69
## ORF55
## ORF5
## ORF9
## ORF37
## ORF75
## ORF16
## ORF13
## ORF71
## ORF12
## ORF72
## ORF6
## ORF41
## ORF60
## ORF54
## ORF52
## ORF57
## ORF35
## ORF10
## ORF15
## ORF27
## ORF62
## ORF48
## ORF35.5
## ORF25
## ORF33
## ORF30
## ORF63
## ORF53
## ORF45
## ORF59
## ORF51
## NOIR_1Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
